Start Again
by xredxrainx
Summary: Sam ran away from Amity Park a long time ago; now, her daughter returns to find her lost mother as well as unravel the mystery of the ghosts beginning to disappear. Both a reformed government sector and local hero, Danny Phantom, appear to be major causes of this. Will Danny Phantom find out why Sam left? And will they stop whatever this organization is working towards...?


**Start Again** **  
** **00.** Prologue

.

.

 _'Just breathe._ ** _Breathe, goddamit!_** ' She flexed her fingers as she sat against the cupboard beneath the sink with a small, white stick in her hand. Never had such a small amount of time - _four minutes!_ \- felt so long. She gritted her teeth, and _hoped_ that what she was testing for was not there. She was unsure as to what she would do… _Really_ unsure. She glanced down at the timer on her phone - only a minute to go, and _god_ it was the longest minute ever.

Finally, the timer went off.

She had flipped the test over so she would not nervously look at it as it started to develop whatever result it was about to hit. The only reason she had bought it was because this _flu_ she has had for a while had not let up, and even then, all the systems were all wrong. She supposed it could have been a bug, but… A part of her decided against it. She rubbed the right side of her neck, the wound from two months ago taking its time to heal. She guessed it made sense; it was no regular wound after all.

She pressed the 'Stop' button on her phone to stop the alarm. She shook nervously before counting down in her head: ' _3… 2… 1…_ '

She turned the test over and paled at the results. ' _Oh no…_ ' her mind went blank for a few minutes, and she sat there, staring at the closed door of her ensuite. She fidgeted with the test, feeling her own future slip away from her grasp. This… It had to be wrong, right? It _had_ to be! Where could she even begin - tell _Danny_? Tell her parents!? She already knew their answer. They already felt like she was a world away from them, and while she _knew_ they cared, would they continue to do so after _this_?

Sam scrambled to her feet, phone and test in tow as she stomped into her room. She flicked the test into a small trash can beside her bed, and unlocked her phone. She supposed she could start with a friend before anyone else.

 **ME:** _you there?_

She already knew the answer to the message, as his PDA was everything but surgically attached to his hip. She nervously played with the sheets of her bed still. For years, Sam had been an anxious girl, never really showing it, but it had always bubbled beneath the surface. She was prone to anxiety attacks and breakdowns, but never had she felt one come on and it _never actually hit her_. That was probably worse.

 **TUCK:** _yeah? what's up sam?_

Oh, how could she word this? _How_? Besides, Tucker was a close friend, but her and him had never been as close as she and Danny. She would have preferred to run to him about this, but considering his involvement with this… well. It was not the right thing, not right now.

 **ME:** _i don't really kno how to say this but…_

Hesitation hit her. She could drop it right then and there and she could sit on it and decide what she was doing? No… that was so cowardly, and she needed someone to know - anyone but her parents and Danny (for now).

 **ME:** _i'm pregnant._

A few minutes passed, and she was unsure if Tucker would even message her back. That made her nervous. Had she just lost a friend because she told him a recently known secret? She hoped not… She feared what her mind would do if she figured that out.

 **TUCK:** _it's danny's?_

' _How-_ '

 **TUCK:** _sam. does he know?_

 **ME:** _no. i just found out just now. don't tell him._

 **TUCK:** _he told me something today. n i think it's gonna make it hard…_

What could he have possibly told Tucker that would make things _harder_?

 **TUCK:** _he asked out_ _paulina_ _today. im sorry. i won't tell him, but…. not rlly sure what you wanna do._

And her heart stopped.

.

Tucker came over probably about an hour after that exchange happened, without Danny. Never had the teen been here without their ghostly friend. Sam was grateful for that. Tucker was sitting on the floor, cross-legged with Sam standing up and facing him. Tears were flooding down her face, and she had given up on trying to wipe them away. She felt pretty damn pathetic, and she just… well, did not know what to do in regards to Danny. Tell him, or not tell him? Still, anger boiled beneath the sadness - she felt used. After they had slept together, they never spoke about it; now two months have passed, and she's carrying a child that is no doubt his. Part of her was spiteful and wanted to keep it a secret. The other part that wanted to keep it secret was the part that cared for him: would he be better of to not know? He would have less issues with Valerie if that's the case…

Tucker watched on, understanding in his navy blue eyes, but he had no advice to give her. Sam understood that as well… She could not blame him. It was not everyday where you found out that your your friend was carrying your best-friend's child. It was a fucked situation, that was the truth.

"Do your parents know yet?" Tucker asked, unable to refrain from asking the question - he had been listening thus far, and Danny _had_ mentioned that him and Sam had slept together, but…

Instantly, she shook her head and promptly buried it in her hands, muttering a few choice swears. She felt rather hopeless, and everything was happening all at once. And she still had to tell her parents, which would not be an easy task.

Tucker stayed quiet for a few moments, checking on his notifications on his phone. He felt bad for Sam, he really did, but this could have been prevented (to an extent) if both of them realised their feelings for each-other. Well, he guessed they did for a moment, considering they had… Tucker blushed at the thought. Danny _had_ told him what had happened, but Danny had decided to put off talking to her about it since he didn't want their relationship to change, which, to Tucker, was a major mistake. He had voiced it too, but Danny being well, Danny, had disagreed and ignored him. Sometimes, Tucker felt he was the only one who could see what was going on.

"You're not going to tell him, are you?" Sam asked softly, glancing up with her head rested against her knee, "I don't want him to know."

Tucker frowned at this. He nearly opened his mouth to say that was a _really_ bad idea, but kept it closed. It was her decision. She was the one carrying the baby, and maybe she did it _for_ Danny. Perhaps she felt that things would be more difficult for him if she said it. Plus, she was no doubt hoping to be _with_ him, but to her that was impossible. And now? Sam no doubt felt _very_ alone.

He crossed his arms and glanced down, taking in the wooden floor he was sitting on, "I won't. Not that I agree with it, but I'll… do what you want. It's your kid."

"It's Danny's too…" Sam mumbled, looking away from him, "I'm not even sure what I'm going to do. How will my parents _react_?"

That, was a question that Tucker could not answer.

.

She wrapped the coat tightly around herself, feeling the cold tickle her flesh as she packed the suitcase into the small brown car she owned. She closed the boot and glanced back up at the home, where no one was there to say farewell to her. Her parents had told her to leave, and that they could not believe she was their daughter. Really, Sam should have seen it coming from a mile away, but it did not meant it did not hurt. She felt like she _had_ left them down, but rage still burned in her chest, and _how dare they_? She already promised herself that she would never do the same things her parents did, such as forcing their views onto her. They were completely different people.

She shivered and hopped into the car, driving to a destination she had no clue of.

.

' _Shit!_ ' she snarled inwardly as she glared down at the flashing red 'E' on her dash.

"May I help you, _dear_?"

She jumped and glanced out the window to see - Vlad. Her eyes narrowed, but she knew she could not run. The half-ghost sniffed and looked quite surprised for a moment, realisation crossing his features. He ' _tsk_ 'ed and opened the door and gestured for her to get out. Quietly, Sam did as she was told. Vlad was a danger to humanity, and he was very much a danger to her now. The ghost stared her over before rubbing his temple.

"It seems Daniel already has an heir, am I correct?" his icy blue eyes gazed down towards her belly, which Sam wrapped her arms around to keep it from his view.

"How do _you_ know?" she spat, "Only three people know, and I remember that _none of them_ have anything to do with you."

Amusement sparkled in his eyes as he crossed his arms, feigning hurt, "Are you implying that I harmed them in order to find information on Daniel?" he gave a dry laugh, before smoothing down his coat, "Of course not. I have a nose. Didn't you know that ghosts have enhanced senses? Or has Daniel kept that secret from you?" He sighed, feigning concern, "Still, my dear, why are you running away from town?"

Horror flooded through Sam the more he spoke. Would he take her as a prisoner now, and wave her in front of Danny in a hope to get him to bow down to Vlad's wants? That was _always_ a possibility. She kept her mouth closed, and eyes off of him. She would not answer any more of his questions. Masters was an evil man who would use any answer she gave in order to cause Danny and everyone _she_ cares about harm.

He gripped her chin roughly, to have her eyes on him, "Tell me, Samantha."

She flinched at both the action and the usage of her full name. _No one_ called her that, as it was clear she hated it. But she was in no position to tell him off, and she kept quiet about it. Still, she knew that she would not be getting out of this situation, and Vlad would get what he wants however he can.

"Well, Danny's dating someone, I got kicked out and have nowhere to go. _And_ like you _implied_ , I'm pregnant. So yes, I'm leaving town - or running away, as you put it," she snapped, venom seeping into her tone.

Vlad pulled back, "Do you have anywhere to go?" he glanced down at the car she had been driving for the last few hours, "Or any money to refuel this?"

What did he care?

"No and no."

Thoughtfulness appeared on his face for a moment as he stepped back and begun pacing. He glanced down at her and sniffed again, nodding to himself before his eyes flickered onto her neck. She had been covering it up, as people would ask about the odd scarring and the faint green glow. She covered it with her hand, blushing slightly at the memory of how she had gotten that scar. ( _"Shit, sorry - I don't know what-" "Shh, it's fine, Danny. It… felt nice? Like warm?"_ ). As soon as the embarrassment came, so did the poignant realisation that that memory was not as happy as she would have wished it to be.

"Fine, I'll offer you a deal, and before you butt in, you will listen to my entire explanation. Or, I'll leave you here and then come for you when you have had the child," he snapped, brushing away some loose white strands of hair, "If your child exhibits ghost powers - which I'm guessing it will - you will hand them to me to train. I will teach them my ways, and… well, whatever happens, happens," Sam felt her lips pull back into a snarl, but Vlad raised his hand, "Nuh uh, Samantha, let me finish. In return, I will allow you whatever you would like. Money, a house… Anything you need to continue your life as needed, and to look after the spawn you are carrying."

Samantha hesitated at the thought of having enough to look after the baby. But at what cost? And he would not make a bet that the child would have ghosts powers if he did not know that they did.

"You're not going to use them for your evil exploits?"

"Of _course_ not! I don't need you running off to Danny about it. I want to train them, and let them choose. If they choose to take the more powerful route of being evil, then so be it. I will be their mentor. If not, then… well. Our paths will cross, no doubt, but as _Masters_ you will still get compensation." Vlad nodded to himself, feeling that Samantha got more out of his deal than even he did - he was sure that she felt the same. Still, when a ghost feels the power, it seems to more than likely to drive them evil, so he has that going for him. Not that Samantha needs to know that, of course. "Now, my dear, what choice would you like to make?"

.

.

 **01.** **Dirty**

.

.

" _Welcome back to our programme. Today, we will be talking with GIW head, Isaac Strong,"_ the audience applauded as the camera focused on a man wearing a white suit with black trimmings. It was messily worn, but seemed to match him. Dark brown hair slicked back, with the sides shaved short, and haunting green eyes stared at the camera with a small smile gracing his lips, " _Now, Isaac, one of the main questions our audience have asked is about Amity. One viewer from that town has asked why has there been such a small amount of ghosts, in contrast to what had been around years ago?_ "

Isaac nodded his head as he listened to the question intently, " _Well, Mike, a decade and a half ago we were considered to be some of the worst ghost hunters. Ever since I was appointed,_ " he smirked this time, clearly enjoying tooting his own horn, " _Our ghost hunting techniques have become more advanced. Now, many of the ghosts have been captured rather than sent back out into the_ other _reality, simply known as the Ghost Zone. And in particular, some ghosts we have a contract with - we don't hunt them, but they hunt for us. One in particular would be Danny Phantom; part-time hunter, part-time hero. We also know of his secret identity, which we are keeping safe for him_."

The interviewer seemed perplexed at the information that was being handed to him, but agreed with whatever Isaac was saying, " _So, has your equipment improved by having these 'hunters' of yours?_ "

" _Of course! They have shared some vital information with us so that we can improve our own weaponry and facilities,"_ Isaac cracked his knuckles before taking a sip of water.

" _Okay, so one more question - with the ghosts now being captured, what will that do to the economy of Amity. That place in particular relies on ghosts for their tourism -"_

" _The people are safe; that is their benefit. Besides, ghosts are so much more mainstream now, that an entire town cannot hope to ride on ghost sightings as a long term business plan._ "

.

Amity Park.

It was a major hotspot for ghosts, and in return, for ghost hunters. It was a place that was considered to be more of a tourist town now, as tourists came through, hoping to catch a glimpse of the ghosts that resided within the town. Much of the town's economy relied on ghosts, although the town had a small-scale bauxite mine. It had been opened half a decade ago, and had been expanding at a quick pace. Its central location in terms of the United States made it a good start for creating alluminium. Many jobs had been created there, but the town still relied heavily on ghosts. But even that, had dropped - it had been ever since Isaac Strong had been appointed as the head of this particular government facility.

The disappearances of ghosts - along with her mother, who was definitely _not_ a ghost - had been what drew the girl the town. Ever since her mother had disappeared four months ago, she had been at a loss. Thankfully, she did have an uncle that lived close-by, but due to his own ghostly status being known by the GIW, he stayed away. The GIW seemed to stay mostly around Amity Park - maybe it was due to how many ghosts came through there. Still, the ghost sightings were dropping by _a lot_.

Newspaper articles showed that the sightings were down by seventy percent, and general searches on the internet proved that particular number was closer to eight-five as of now. The girl tapped her fingers against the surface of her laptop before she closed it and leaned back. The school library was one of her few sanctuaries from the outside world, and what was going on in her suddenly turbulent life. Still, she had studying to do, as she glanced over at the sheets of paper that were her Biology assignment.

Researching chimpanzees and bonobos. She was interested in the topic somewhat, but she had no motivation to start it right then and there. Motivation was a rarity for her, considering how much her _other_ life was spiralling out of control.

"Whatcha doin' here, Lili?"

She blinked twice and glanced up to see Damien; he was a blonde-haired boy with gorgeous green eyes. He was wearing his usual smirk as he sat down beside her. He was one of her closer friends, but even he had no clue of the secrets she kept to herself.

"Studying."

It wasn't exactly a lie.

Boredom crossed his features for a moment before he gestured for the assignment she was skimming over. She handed it over, and he glanced over it before his nose scrunched up. He had faint freckles over his golden skin, and his green eyes were _definitely_ his most notable feature. He was wearing rather casual clothes for the cool weather; white shirt with a black hoodie, and grey jeans with a brown and gold belt.

"Sounds kinda boring," he drawled, grinning at her, "C'mon. It's the start of a _long_ weekend - three days off, you know? Act like your age for once?"

Right. Long weekend. Monday was the day off. That would give her time to scan around the town without having to worry about being too tired to keep her eyes open during school. Plus side with not having her parent around would be that if she _really_ needed, she could take the day off. Considering her situation, the school does not ask about it. Still, it was her uncle that convinced them that she was fine without her mother. So, that was the only reason she was not in the system now. Although, throwing her in foster care would be a waste of everyone's time.

"How about…" she pretended to think for a moment, "no? This _is_ due next week, you know?"

"And? You're like the queen of finishing assignments late minute and still _passing_?"

Because a C minus was something to be _proud_ of. Her grades had suffered big time, and it was apparently her 'natural ability' that kept her going. Still, Damien did have a point. Maybe she should let her hair down for the next few days and _relax_. She had barely gotten any of that during the last four months; it had felt _wrong_ to rest when her mother was out there, possibly having the worst of things being done to her.

"... I'll think about it," she answered after a moment of silence.

Damien was a kind soul, even though he was a bit spoiled at times. The boy's face erupted with a grin, as if he had won the lottery. Right.

.

Blue flames licked the sides of her body as her dangled down, green eyes on the other ghost before her. Phantom was watching over her, thermos already in hand. She bared her teeth at him, snarling lowly, "So _what_ you're going to take me away like the others? How can't you see the damage that you're causing to our _home_ from what you're doing?"

Phantom lowered to her level, his feet touching down as he walked over to her, standing above her. Ember had seen that the 'ghost child' had now grown into a man, but he had none of the realisations of an adult. Or maybe he did, but Ember could not care _less_ about what he was feeling. The Ghost Zone was being torn apart, and it was so _hard_ to stay there, but due to their reliance on the energy there, a ghost - a _full_ ghost - could not be without the Ghost Zone for long. When she had first heard that the others were disappearing, she had just found amusement out of it. Now? It was horrible. She knew where they were going, and who knows if any that were caught were still alive.

The halfa gripped the thermos tightly, glowing green eyes flickering unto her, "It is a means to an end, you know. Once you all are gone, _I'm_ free."

Ember let out a hollow laugh, "So this time it's selfishness," she stood up shakily, feeling the green ooze slipping from the wounds he had caused - he had become a lot more powerful now, she had to give him that, "The high and mighty hero, now attacking others because he needs to escape. Jeez. I wonder what Frostbite and Pandora would think of this? Oh _wait_ , your friends have taken them away. I guess friendship means jack shit, am I right?"

"Like you'd understand. I _tried_ to stop them from doing what they're doing, but I can't stop them. Not like this," Phantom said, opening the lid of the thermos.

"Right, _right_. To save your stupid little identity?" she watched in amusement as his eyes went wide, "Yes, I remember. Those government _idiots_ cleared everyone's minds, right? Now, they hold that over _your_ head, so you do their begging like a little _puppy_. Congrats. The great _hero_ of Amity Park is now reduced to some government _dog_ just because he's piss scared his own secret will get out. _Who cares_? They accepted you then - the public - so what does it matter?"

Phantom let out a feral snarl, baring his fangs at the other ghost, "Shut the hell up. Most of you _are_ evil anyways - so what does it matter? I'm still keeping Amity safe."

And with that, Ember felt her weakened body being sucked into the thermos, although she _swore_ she heard a small 'sorry' as her world went black.

.

Danny Fenton found his way down to the basement, thermos still in hand from earlier. It was empty now, and he placed it on charge. It was an instant charge, so he was able to take it back right up. He had made his way to his parents to visit them. His blue eyes flickered onto the portal into the Ghost Zone. One of the main conditions the GIW had laid onto him was that he was not to go into the portal unless he was given strict instructions to do so. His eyes narrowed. Did they not realize that while he was not a _full_ ghost, he still needed to go into there and absorb the weird energy that dwelled within?

Of course not.

All they cared about was finding all the weaknesses a ghost had. Hence why he was their 'dog' as Ember had so kindly put it. Still, her words had struck a chord within him. What _was_ he doing? Did his identity matter more than all the ghosts? Even his _friends_. He was sure that all the 'good' ghosts hated him from hell and back. Still, from memory of the 'check list' in the main hall of the GIW building, not many ghosts were left in the other dimension. Clockwork was among some of the few, although Danny knew that that particular ghost would not leave the Ghost Zone unless things were really dire.

Maybe that was why Danny kept going on this path. Clockwork _would_ intervene if what he was doing would lead to disaster, right?

That was not a question that even Danny could answer anymore. Maybe Clockwork had given up, and was just going to let the timeline meet its course. Maybe that was a good thing.

.

Lilith stretched her hands over her head the moment she dropped her heavy bags onto the marble counter. The house she was currently staying in was being paid for by her uncle. He had been rather kind with everything that was going on. For a long time, he had visited her and her mother. It was an odd sort of relationship, considering Lilith knew that she was not actually related to her uncle. It had just been something she grew up with, and a familial connection had been built in that way.

Still… she did feel alone when she got home. She was still used to seeing her mother work on some report that she would have gotten from her office, and then explain in detail what it all meant to Lilith. Oddly enough, she understood that. Science came easily to her, although nothing else really _clicked_ in that sort of way. But even with her little secret and the hunt for her mother, her science skills had slowly become less prevalent.

"Lili!"

The girl jumped and turned over to see her uncle.

She grinned widely and jumped into his arms, surprised by his sudden appearance.

"Uncle Vlad!"

.

 _tbc._

.

Hey there. So this is hopefully going to turn out well. I'm going to try and the perspective on both Danny and Lilith as much as I can. For now, it will be mainly on Lilith to get her character a bit more established (along with others I will be introducing further on). I'm a bit horrid with updating, so forgive me for that; work, other life engagements you know. I'm not the best at editing, so hopefully there's nothing _major_ in terms of editing errors. Also, I can't do summaries for shit - I don't want to give away too much of the plot either… considering there are some mysteries in here, me thinks. Anyways, I hope this was enjoyable, and this is a shorter chapter in contrast to what I would normally write, so expect a larger update next time around.

 **Please know that this version of this story has been put into a 'cleaner' version, as I am wanting to abide by this site's rules. The not so clean version will be found on AO3, when we get to that point. This story will still have those topics discussed, but not nearly to the same extent and the rating may change, if I feel it needs to.**


End file.
